TRANNY SLIPPING

I'm having trouble with my 95 trooper. The check engine light comes on after it is driven about 10 miles and doesnt go off. The transmission recently started slipping in the lower gears and wont easily shift into the higher gears without reving up, (which I dont do). Once you get going it seems to be ok but it takes forever to get up to speed. We just had a 90,000 service on it. They replaced the oil filter and oil, transmission 2 part kit & filter air and fuel filter. During inspection they found both axle boots ripped, lower ball joints out, oil cooler lines leaking, oil switch leaking. They also recomend spark plugs and wires and brakes. We just replaced the brakes and pads 4 months ago. They said the tranny is slipping but didnot check the codes or say what was wrong as we thought they would. Any ideas on what I can do? Or what might be wrong? I just bought this rig 2 years ago and it is not driven under harsh conditions. I have pulled cars and trailers with it but nothing heavy. Is my tranny going out and need to be replaced or could it just need a better service? I heard there is a filter or screen in the tranny, could that be clogged and make it not want to shift properly? Please help, this is my only vehicle and I cant have it go down on me. Thank you for any advice you can give. : )